1XWV - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   STRUCTURE OF THE HOUSE DUST MITE ALLERGEN DER F 2: IMPLICATIONS FOR FUNCTION AND MOLECULAR BASIS OF IGE CROSS-REACTIVITY

Authors :   B. R. Johannessen, L. K. Skov, J. S. Kastrup, O. Kristensen, C. Bolwig, J. N. Larsen, M. Spangfort, K. Lund, M. Gajhede

Date :   02 Nov 04 (Deposition) - 14 Dec 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.83

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)

Keywords :   Beta Sheets, Allergen (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   B. R. Johannessen, L. K. Skov, J. S. Kastrup, O. Kristensen, C. Bolwig, J. N. Larsen, M. Spangfort, K. Lund, M. Gajhede
Structure Of The House Dust Mite Allergen Der F 2: Implications For Function And Molecular Basis Of Ige Cross-Reactivity.
Febs Lett. V. 579 1208 2005
PubMed-ID: 15710415 | Reference-DOI: 10.1016/J.FEBSLET.2004.11.115
(for further references see the PDB file header)

Molecule 1 - DER F II
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	PICHIA PASTORIS
	Expression System Plasmid	:	PGAPZALPHA-A
	Expression System Taxid	:	4922
	Expression System Vector Type	:	PLASMID
	Organism Common	:	AMERICAN HOUSE DUST MITE
	Organism Scientific	:	DERMATOPHAGOIDES FARINAE
	Organism Taxid	:	6954
	Synonym	:	MITE ALLERGEN DER F II

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 2)

No.	Name	Count	Type	Full Name
1	PE3	1	Ligand/Ion	3,6,9,12,15,18,21,24,27,30,33,36,39-TRIDECAOXAHENTETRACONTANE-1,41-DIOL
2	XPE	1	Ligand/Ion	3,6,9,12,15,18,21,24,27-NONAOXANONACOSANE-1,29-DIOL

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	PE3	1	Ligand/Ion	3,6,9,12,15,18,21,24,27,30,33,36,39-TRIDECAOXAHENTETRACONTANE-1,41-DIOL
2	XPE	-1	Ligand/Ion	3,6,9,12,15,18,21,24,27-NONAOXANONACOSANE-1,29-DIOL

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	PE3	-1	Ligand/Ion	3,6,9,12,15,18,21,24,27,30,33,36,39-TRIDECAOXAHENTETRACONTANE-1,41-DIOL
2	XPE	1	Ligand/Ion	3,6,9,12,15,18,21,24,27-NONAOXANONACOSANE-1,29-DIOL

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:4 , VAL A:18 , CYS A:27 , PHE A:35 , LEU A:37 , ILE A:54 , ASP A:64 , PRO A:66 , ALA A:88 , TYR A:90 , TRP A:92 , PRO A:95 , ILE A:97 , VAL A:108 , ALA A:122 , HIS A:124 , ALA A:125 , ILE B:97 , PRO B:99	BINDING SITE FOR RESIDUE PE3 A 1001
2	AC2	SOFTWARE	ASP B:4 , CYS B:27 , ILE B:29 , PHE B:35 , LEU B:37 , ALA B:39 , ILE B:52 , TYR B:90 , TRP B:92 , ALA B:122 , THR B:123 , HIS B:124	BINDING SITE FOR RESIDUE XPE B 1002

Asymmetric Unit

No.	Residues
1	A:8	-	A:119
2	A:21	-	A:27
3	A:73	-	A:78
4	B:8	-	B:119
5	B:21	-	B:27
6	B:73	-	B:78

Asymmetric Unit

No.	Residues
1	Cys A:78	-	Pro A:79
2	Cys B:78	-	Pro B:79

Asymmetric Unit (4, 8)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_ALL2_DERFA_001 *	M	93	V	ALL2_DERFA	---	---	A/B	M	76	V
2	UniProt	VAR_ALL2_DERFA_002 *	I	105	A	ALL2_DERFA	---	---	A/B	A	88	A
3	UniProt	VAR_ALL2_DERFA_003 *	I	128	V	ALL2_DERFA	---	---	A/B	V	111	V
4	UniProt	VAR_ALL2_DERFA_004 *	G	142	A	ALL2_DERFA	---	---	A/B	A	125	A
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 1 (4, 4)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_ALL2_DERFA_001 *	M	93	V	ALL2_DERFA	---	---	A	M	76	V
2	UniProt	VAR_ALL2_DERFA_002 *	I	105	A	ALL2_DERFA	---	---	A	A	88	A
3	UniProt	VAR_ALL2_DERFA_003 *	I	128	V	ALL2_DERFA	---	---	A	V	111	V
4	UniProt	VAR_ALL2_DERFA_004 *	G	142	A	ALL2_DERFA	---	---	A	A	125	A
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 2 (4, 4)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_ALL2_DERFA_001 *	M	93	V	ALL2_DERFA	---	---	B	M	76	V
2	UniProt	VAR_ALL2_DERFA_002 *	I	105	A	ALL2_DERFA	---	---	B	A	88	A
3	UniProt	VAR_ALL2_DERFA_003 *	I	128	V	ALL2_DERFA	---	---	B	V	111	V
4	UniProt	VAR_ALL2_DERFA_004 *	G	142	A	ALL2_DERFA	---	---	B	A	125	A
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(no "PROSITE Motif" information available for 1XWV)

(no "Exon" information available for 1XWV)

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:129
 aligned with ALL2_DERFA | Q00855 from UniProtKB/Swiss-Prot  Length:146

    Alignment length:129
                                    27        37        47        57        67        77        87        97       107       117       127       137         
           ALL2_DERFA    18 DQVDVKDCANNEIKKVMVDGCHGSDPCIIHRGKPFTLEALFDANQNTKTAKIEIKASLDGLEIDVPGIDTNACHFMKCPLVKGQQYDIKYTWNVPKIAPKSENVVVTVKLIGDNGVLACAIATHGKIRD 146
               SCOP domains d1xwva_ A: Major mite allergen                                                                                                    SCOP domains
               CATH domains 1xwvA00 A:1-129  [code=2.60.40.770, no name defined]                                                                              CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....ee.....eeeeee........eeee...eeeeeeeee........eeeeeeee..eee.......hhhhh.........eeeeeeeee..........eeeeeeeee..eeeeeeee..eeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------V-----------A----------------------V-------------A---- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xwv A   1 DQVDVKDCANNEIKKVMVDGCHGSDPCIIHRGKPFTLEALFDANQNTKTAKIEIKASLDGLEIDVPGIDTNACHFMKCPLVKGQQYDAKYTWNVPKIAPKSENVVVTVKLVGDNGVLACAIATHAKIRD 129
                                    10        20        30        40        50        60        70        80        90       100       110       120

Chain B from PDB  Type:PROTEIN  Length:129
 aligned with ALL2_DERFA | Q00855 from UniProtKB/Swiss-Prot  Length:146

    Alignment length:129
                                    27        37        47        57        67        77        87        97       107       117       127       137         
           ALL2_DERFA    18 DQVDVKDCANNEIKKVMVDGCHGSDPCIIHRGKPFTLEALFDANQNTKTAKIEIKASLDGLEIDVPGIDTNACHFMKCPLVKGQQYDIKYTWNVPKIAPKSENVVVTVKLIGDNGVLACAIATHGKIRD 146
               SCOP domains d1xwvb_ B: Major mite allergen                                                                                                    SCOP domains
               CATH domains 1xwvB00 B:1-129  [code=2.60.40.770, no name defined]                                                                              CATH domains
           Pfam domains (1) E1_DerP2_DerF2-1xwvB01 B:1-125                                                                                               ---- Pfam domains (1)
           Pfam domains (2) E1_DerP2_DerF2-1xwvB02 B:1-125                                                                                               ---- Pfam domains (2)
         Sec.struct. author .....ee.....eeeeee........eeee...eeeeeeeee........eeeeeeee..eee.......hhhhh.........eeeeeeeee..........eeeeeeeee..eeeeeeee..eeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------V-----------A----------------------V-------------A---- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xwv B   1 DQVDVKDCANNEIKKVMVDGCHGSDPCIIHRGKPFTLEALFDANQNTKTAKIEIKASLDGLEIDVPGIDTNACHFMKCPLVKGQQYDAKYTWNVPKIAPKSENVVVTVKLVGDNGVLACAIATHAKIRD 129
                                    10        20        30        40        50        60        70        80        90       100       110       120

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: Immunoglobulin-like beta-sandwich (7299)

Superfamily: E set domains (509)

Family: ML domain (9)

Protein domain: Major mite allergen (7)

House-dust mite (Dermatophagoides farinae), Der f 2 [TaxId: 6954] (5)

1a	d1xwva_	A:
1b	d1xwvb_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Sandwich (5577)

Topology: Immunoglobulin-like (3897)

Homologous Superfamily: [code=2.60.40.770, no name defined] (9)

American house dust mite (Dermatophagoides farinae) (5)

1a	1xwvA00	A:1-129
1b	1xwvB00	B:1-129

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: E1_DerP2_DerF2] (8)

Family: E1_DerP2_DerF2 (8)

Dermatophagoides farinae (American house dust mite) (2)

1a	E1_DerP2_DerF2-1xwvB01	B:1-125
1b	E1_DerP2_DerF2-1xwvB02	B:1-125

Asymmetric Unit(hide GO term definitions)

Chain A,B (ALL2_DERFA | Q00855)

cellular component
	GO:0005576		extracellular region		The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

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Description

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Chains, Units

Ligands, Modified Residues, Ions (2, 2)

Sites (2, 2)

SS Bonds (6, 6)

Cis Peptide Bonds (2, 2)

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